Ancestral genomic functional differences in oligodendroglia: implications for Alzheimer's disease

Abstract

Introduction: This study investigates ancestry-specific changes in induced pluripotent stem cell (iPSC)-derived oligodendroglia genomic regulation in Alzheimer's disease (AD), addressing diversity gaps by including African, Amerindian, and European ancestries in the analysis.

Methods: We generated 12 iPSC lines from AD patients and controls with different apolipoprotein E (APOE) genotypes, APOE ε3/ ε3 and APOE ε4/ ε4, across three ancestries. Lines were differentiated into neural spheroids containing oligodendrocyte lineage cells and analyzed by single-nucleus RNA sequencing, Assay for Transposase-Accessible Chromatin with sequencing (ATACseq)APO, and High-throughput Chromosome Conformation Capture (Hi-C).

Results: We identified ancestry-specific differences in gene expression and chromatin accessibility of AD genome-wide association study candidate genes. APOE ε4/ ε4 carriers across all ancestries showed upregulated cholesterol biosynthesis genes with decreased myelination markers. iPSC-derived oligodendrocytes demonstrated high correlation (R² > 0.85) with human brain transcriptomes.

Discussion: Our findings highlight the importance of studying diverse ancestries in AD research and suggest early APOE ε4 effects on cholesterol metabolism. The validated iPSC model provides a valuable tool for investigating ancestry-specific disease mechanisms.

Highlights: First study comparing iPSC-derived oligodendroglia across three ancestries. APOE ε4 carriers show upregulated cholesterol synthesis in oligodendroglia. Reduced myelin gene expression observed in APOE ε4/ε4 oligodendroglia. Ancestry-specific differences found in AD GWAS genes and chromatin states. Novel insights into oligodendrocyte biology relevant to Alzheimer's disease.

Keywords: APOE ε4/ ε4 genotype; ATAC sequencing; Alzheimer's disease (AD); RNA sequencing; ancestry‐specific regulation; cholesterol biosynthesis; chromatin accessibility; induced pluripotent stem cells (iPSCs); myelination; oligodendrocytes.

FIGURE 1

Characterization of induced pluripotent stem cell (iPSC)‐derived neural spheroids with different ancestral backgrounds. (A) Representative image of immunocytochemistry analysis of iPSC‐derived neural three‐dimensional (3D) cultures. Scale bar: 100 µm. (B) Visualization of single‐nucleus clusters from 47,898 nuclei integrated across 12 samples of iPSC‐derived neural 3D cultures including four samples from each ancestry (AF, AI, EU). Clustering of single nuclei from the integrated datasets representing the identified cellular clusters based on scRNA‐seq data and grouped by cell type. (C) Visualization of different cell marker expressions in different cell clusters shown in panel (B). Cells are expression depicted from gray (low) to purple (high).

FIGURE 2

Transcriptional changes in oligodendroglia based on apolipoprotein E (APOE) genotype. Differential gene expression occurring in oligodendroglia based on APOE genotype, comparing APOE ε3/ ε3 lines to APOE ε4/ ε4 lines, irrespective of ancestry. (A) Volcano plot showing differentially expressed genes (DEGs) between APOE ε3/ ε3 and APOE ε4/ ε4 samples in iPSC‐derived oligodendrocyte progenitor cells (iOPC) cluster. Genes that have been reported as Alzheimer's disease (AD) genome‐wide association study (GWAS) hits are labeled. (B) Dot plot illustrating pseudo‐bulk expression of differentially expressed AD GWAS hits in iOPC cluster. (C) Volcano plot showing differentially expressed genes between APOE ε3/ ε3 and APOE ε4/ ε4 samples in iPSC‐derived oligodendrocyte (iOL)ε cluster. Genes that have been reported as AD GWAS hits are labeled. (D) Dot plot illustrating pseudo‐bulk expression of differentially expressed AD GWAS hits in iOL cluster.

FIGURE 3

Differential expression of genes implicated in cholesterol biosynthesis and myelination between induced pluripotent stem cell‐derived oligodendrocyte progenitor cells with different APOE genotypes. Dot plot illustrates pseudo‐bulk expression of differentially expressed genes (p value adj < 0.05 and fold change > 1 or ← 1).

FIGURE 4

Visualization of single‐nucleus clusters from 76,409 nuclei integrated across 12 samples of induced pluripotent stem cell‐derived neural three‐dimensional cultures including four samples from each ancestry (AF, AI, EU). (A) Clustering of single nuclei from integrated datasets representing identified cellular clusters based on Assay for Transposase‐Accessible Chromatin Sequencing (ATAC‐seq) data. (B) Visualization of oligodendroglia markers expression in the different cell clusters shown in panel (A). Accessibility depicted from purple (low) to yellow (high).

FIGURE 5

Chromatin accessibility and Hi‐C loops overview for a subregion of FGF12 in oligodendroglia of different ancestries. Highlighted in yellow is a differentially accessible region between ancestries with a profile that correlates with FGF12 expression.

FIGURE 6

Comparative analysis of differentially expressed genes (DEGs) and genes with differentially accessible regions (DARs) in oligodendroglia based on apolipoprotein E (APOE) genotype and Alzheimer's disease status. (A and B) Comparison of APOE ε3/ ε3 oligodendrocyte progenitor cells (OPCs) to APOE ε4/ ε4 OPCs. (C and D) Comparison of APOE ε3/ ε3 oligodendrocytes to APOE4/4 oligodendrocytes. (E and F) Comparison of OPCs from affected donors to non‐cognitively impaired donors OPCs. (G and H) Comparison of oligodendrocytes from affected donors to oligodendrocytes from unaffected controls.